A Data-Parallel Molecular Dynamics Method for Liquids with Coulombic Interactions

Hedman, Fredrik; Laaksonen, Aatto

doi:10.1080/08927029508022020

Cited by 9 publications

(6 citation statements)

References 33 publications

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“…As the number of particles in the system grows we often combine the calculation of the short‐range part of van der Waals potential with the real‐space part of electrostatic interactions by using a same cutoff. With this choice, the reciprocal‐space parts of the Ewald summation method become the most time‐consuming part to be calculated …”

Section: Tests For Accuracy and Performancementioning

confidence: 99%

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Accelerating electrostatic interaction calculations with graphical processing units based on new developments of ewald method using non‐uniform fast fourier transform

et al. 2015

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We present new algorithms to improve the performance of ENUF method (F. Hedman, A. Laaksonen, Chem. Phys. Lett. 425, 2006, 142) which is essentially Ewald summation using Non-Uniform FFT (NFFT) technique. A NearDistance algorithm is developed to extensively reduce the neighbor list size in real-space computation. In reciprocal-space computation, a new algorithm is developed for NFFT for the evaluations of electrostatic interaction energies and forces. Both real-space and reciprocal-space computations are further accelerated by using graphical processing units (GPU) with CUDA technology. Especially, the use of CUNFFT (NFFT based on CUDA) very much reduces the reciprocal-space computation. In order to reach the best performance of this method, we propose a procedure for the selection of optimal parameters with controlled accuracies. With the choice of suitable parameters, we show that our method is a good alternative to the standard Ewald method with the same computational precision but a dramatically higher computational efficiency.

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Section: Tests For Accuracy and Performancementioning

confidence: 99%

“…With this choice, the reciprocal-space parts of the Ewald summation method become the most time-consuming part to be calculated. [52,53] When d and r c are fixed, Ewald parameter a is determined by eq. (16), and then k c by eq.…”

Section: Tests For Accuracy and Performancementioning

confidence: 99%

Accelerating electrostatic interaction calculations with graphical processing units based on new developments of ewald method using non‐uniform fast fourier transform

et al. 2015

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“…This method achieved a near linear speedup of 7.7 on 8 processors for a benchmark system of one molecule of echistatin, a small peptide with 713 atoms, one chloride ion and 6903 water molecules [41]. Two other similar algorithms appear in the literature, both for single instruction multiple data (SJMD) architectures, one for the Connection Machine CM-200 [74] and another for a MasPar NIP-2 [75] although few details are provided in either case.…”

Section: Spatial Parallel Molecular Dvnamics Algorithmmentioning

confidence: 99%

Parallel atomistic simulations

Heffelfinger

2000

Computer Physics Communications

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“…This implies that we need to choose a real-space cut-off about the same size as the short-range cut-off. With this nonoptimal choice, the reciprocal-space parts of the Ewald summation method become the most time-consuming to calculate [55].…”

Section: Fast Ewald Summationmentioning

confidence: 99%

“…These parameters are correlated with each other through two conditions shown in Equations (54) and (55). With required accuracy parameter n .…”

mentioning

confidence: 99%

Non-Uniform FFT and Its Applications in Particle Simulations

Wang¹,

Hedman²,

Porcu³

et al. 2014

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A Data-Parallel Molecular Dynamics Method for Liquids with Coulombic Interactions

Cited by 9 publications

References 33 publications

Accelerating electrostatic interaction calculations with graphical processing units based on new developments of ewald method using non‐uniform fast fourier transform

Accelerating electrostatic interaction calculations with graphical processing units based on new developments of ewald method using non‐uniform fast fourier transform

Parallel atomistic simulations

Non-Uniform FFT and Its Applications in Particle Simulations

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